Validation of crystallographic models containing TLS or other descriptions of anisotropy
The use of TLS (translation/libration/screw) models to describe anisotropic displacement of atoms within a protein crystal structure has become increasingly common. These models may be used purely as an improved methodology for crystallographic refinement or as the basis for analyzing inter‐domain a...
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| Veröffentlicht in: | Acta crystallographica. Section D, Biological crystallography. Biological crystallography., 2010-08, Vol.66 (8), p.889-900 |
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| container_title | Acta crystallographica. Section D, Biological crystallography. |
| container_volume | 66 |
| creator | Zucker, Frank Champ, P. Christoph Merritt, Ethan A. |
| description | The use of TLS (translation/libration/screw) models to describe anisotropic displacement of atoms within a protein crystal structure has become increasingly common. These models may be used purely as an improved methodology for crystallographic refinement or as the basis for analyzing inter‐domain and other large‐scale motions implied by the crystal structure. In either case it is desirable to validate that the crystallographic model, including the TLS description of anisotropy, conforms to our best understanding of protein structures and their modes of flexibility. A set of validation tests has been implemented that can be integrated into ongoing crystallographic refinement or run afterwards to evaluate a previously refined structure. In either case validation can serve to increase confidence that the model is correct, to highlight aspects of the model that may be improved or to strengthen the evidence supporting specific modes of flexibility inferred from the refined TLS model. Automated validation checks have been added to the PARVATI and TLSMD web servers and incorporated into the CCP4i user interface. |
| doi_str_mv | 10.1107/S0907444910020421 |
| format | Article |
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In either case validation can serve to increase confidence that the model is correct, to highlight aspects of the model that may be improved or to strengthen the evidence supporting specific modes of flexibility inferred from the refined TLS model. 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Christoph</creatorcontrib><creatorcontrib>Merritt, Ethan A.</creatorcontrib><title>Validation of crystallographic models containing TLS or other descriptions of anisotropy</title><title>Acta crystallographica. Section D, Biological crystallography.</title><addtitle>Acta Cryst. D</addtitle><description>The use of TLS (translation/libration/screw) models to describe anisotropic displacement of atoms within a protein crystal structure has become increasingly common. These models may be used purely as an improved methodology for crystallographic refinement or as the basis for analyzing inter‐domain and other large‐scale motions implied by the crystal structure. In either case it is desirable to validate that the crystallographic model, including the TLS description of anisotropy, conforms to our best understanding of protein structures and their modes of flexibility. A set of validation tests has been implemented that can be integrated into ongoing crystallographic refinement or run afterwards to evaluate a previously refined structure. In either case validation can serve to increase confidence that the model is correct, to highlight aspects of the model that may be improved or to strengthen the evidence supporting specific modes of flexibility inferred from the refined TLS model. Automated validation checks have been added to the PARVATI and TLSMD web servers and incorporated into the CCP4i user interface.</description><subject>ANISOTROPY</subject><subject>ATOMS</subject><subject>CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY</subject><subject>Confidence</subject><subject>CRYSTAL STRUCTURE</subject><subject>Crystallography</subject><subject>Crystallography, X-Ray - methods</subject><subject>Databases, Protein</subject><subject>DEPOSITION</subject><subject>Descriptions</subject><subject>Displacement</subject><subject>FLEXIBILITY</subject><subject>INTERFACES</subject><subject>Internet</subject><subject>Models, Chemical</subject><subject>PROTEIN STRUCTURE</subject><subject>PROTEINS</subject><subject>RECOMMENDATIONS</subject><subject>Research Papers</subject><subject>TLS models</subject><subject>Translations</subject><subject>VALIDATION</subject><issn>1399-0047</issn><issn>0907-4449</issn><issn>1399-0047</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2010</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkc1u1DAURiMEoqXwAGxQJBZ0E7j-i-0NUlVKgY6gUocprCyP7cwYMnGwPcC8PYlSRkVIsLItn_NdX9-ieIzgOULAX1yBBE4plQgAA8XoTnGIiJQVAOV3b-0PigcpfYGBwoTfLw4w1JLUQhwWnxa69VZnH7oyNKWJu5R124ZV1P3am3ITrGtTaUKXte98tyrns6syxDLktYuldclE3496Gn3d-RRyDP3uYXGv0W1yj27Wo-Lj67P56Ztq9uH87enJrDKM1lCJZQPC2AZL3BAOjRBNo4kUtRFGcsqWGkutqQRn0bImyDLJDKotsZphZIEcFS-n3H673DhrXJejblUf_UbHnQraqz9vOr9Wq_BdYYk45mwIeDoFhJS9SsZnZ9ZDv50zWQ3_xRBGeKCe3ZSJ4dvWpaw2PhnXtrpzYZsUp0IyiWEkj_9JopojzLiAsTSaUBNDStE1-2cjUOOE1V8THpwnt_vdG79HOgBiAn741u3-n6hOPr-6uGbDYVCrSfUpu597VcevquaEM3X9_lwtLt_NLxcLqi7IL2KswXE</recordid><startdate>201008</startdate><enddate>201008</enddate><creator>Zucker, Frank</creator><creator>Champ, P. 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Christoph ; Merritt, Ethan A.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c5460-8bf08cdf292f370f88ffa3986c8c9745ba29aa490ed1b631d595c16d3da521d03</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2010</creationdate><topic>ANISOTROPY</topic><topic>ATOMS</topic><topic>CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY</topic><topic>Confidence</topic><topic>CRYSTAL STRUCTURE</topic><topic>Crystallography</topic><topic>Crystallography, X-Ray - methods</topic><topic>Databases, Protein</topic><topic>DEPOSITION</topic><topic>Descriptions</topic><topic>Displacement</topic><topic>FLEXIBILITY</topic><topic>INTERFACES</topic><topic>Internet</topic><topic>Models, Chemical</topic><topic>PROTEIN STRUCTURE</topic><topic>PROTEINS</topic><topic>RECOMMENDATIONS</topic><topic>Research Papers</topic><topic>TLS models</topic><topic>Translations</topic><topic>VALIDATION</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Zucker, Frank</creatorcontrib><creatorcontrib>Champ, P. 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Section D, Biological crystallography.</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Zucker, Frank</au><au>Champ, P. Christoph</au><au>Merritt, Ethan A.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Validation of crystallographic models containing TLS or other descriptions of anisotropy</atitle><jtitle>Acta crystallographica. Section D, Biological crystallography.</jtitle><addtitle>Acta Cryst. D</addtitle><date>2010-08</date><risdate>2010</risdate><volume>66</volume><issue>8</issue><spage>889</spage><epage>900</epage><pages>889-900</pages><issn>1399-0047</issn><issn>0907-4449</issn><eissn>1399-0047</eissn><abstract>The use of TLS (translation/libration/screw) models to describe anisotropic displacement of atoms within a protein crystal structure has become increasingly common. These models may be used purely as an improved methodology for crystallographic refinement or as the basis for analyzing inter‐domain and other large‐scale motions implied by the crystal structure. In either case it is desirable to validate that the crystallographic model, including the TLS description of anisotropy, conforms to our best understanding of protein structures and their modes of flexibility. A set of validation tests has been implemented that can be integrated into ongoing crystallographic refinement or run afterwards to evaluate a previously refined structure. In either case validation can serve to increase confidence that the model is correct, to highlight aspects of the model that may be improved or to strengthen the evidence supporting specific modes of flexibility inferred from the refined TLS model. 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| ispartof | Acta crystallographica. Section D, Biological crystallography., 2010-08, Vol.66 (8), p.889-900 |
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| source | MEDLINE; Wiley Online Library All Journals; Alma/SFX Local Collection |
| subjects | ANISOTROPY ATOMS CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY Confidence CRYSTAL STRUCTURE Crystallography Crystallography, X-Ray - methods Databases, Protein DEPOSITION Descriptions Displacement FLEXIBILITY INTERFACES Internet Models, Chemical PROTEIN STRUCTURE PROTEINS RECOMMENDATIONS Research Papers TLS models Translations VALIDATION |
| title | Validation of crystallographic models containing TLS or other descriptions of anisotropy |
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